3700 (G > A)

General info

Chr
chrM
Start
3700
End
3700
Ref
G
Alt
A
Mitimpact ID
MI.11574
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
394
AA pos
132
AA ref
A
AA alt
T
Codon substitution
Gca/Aca
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Conservation

PhyloP 100v
-4.15 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Disease causing automatic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
Pathogenic
ClinVar March2020 ClnDBN
Abnormal electroretinogram;

visual loss;

leber's optic atrophy;

optic neuropathy
ClinVar March2020 ClnAllele ID
76427
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0000512, medgen:c0476397;

human phenotype ontology:hp:0000572, medgen:c3665386;

human phenotype ontology:hp:0001112, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

human phenotype ontology:hp:0001138, medgen:c3887709
MITOMAP Allele
MITOMAP Phenotype
Lhon
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
-
MITOMAP Status
Cfrm
MITOMAP NRef
5
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.15 CPD variant frequency
AA ref
A
CPD AA alt
T
Aln pos
133
RefSeq protein ID
Species name
Pongo pygmaeus
Ncbi taxon ID

3700 (G > C)

General info

Chr
chrM
Start
3700
End
3700
Ref
G
Alt
C
Mitimpact ID
MI.11572
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
394
AA pos
132
AA ref
A
AA alt
P
Codon substitution
Gca/Cca
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Conservation

PhyloP 100v
-4.15 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

3700 (G > T)

General info

Chr
chrM
Start
3700
End
3700
Ref
G
Alt
T
Mitimpact ID
MI.11573
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
394
AA pos
132
AA ref
A
AA alt
S
Codon substitution
Gca/Tca
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Powered by MitoWheel

Conservation

PhyloP 100v
-4.15 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
Low impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Deleterious Score and details of the predictor
SNAP
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Neutral Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
Meta SNP
Neutral Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 3700 (G/A) 3700 (G/C) 3700 (G/T)
~ 3700 (Gca/Aca) 3700 (Gca/Cca) 3700 (Gca/Tca)
Chr chrM chrM chrM
Start 3700 3700 3700
End 3700 3700 3700
Ref G G G
Alt A C T
MitImpact id MI.11574 MI.11572 MI.11573
Gene symbol MT-ND1 MT-ND1 MT-ND1
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Uniprot id P03886 P03886 P03886
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
Gene position 394 394 394
AA position 132 132 132
AA ref A A A
AA alt T P S
Codon substitution Gca/Aca Gca/Cca Gca/Tca
PhyloP 100V -4.15 -4.15 -4.15
PhastCons 100V 0 0 0
PolyPhen2 benign probably_damaging possibly_damaging
PolyPhen2 score 0.15 0.97 0.78
SIFT neutral neutral neutral
SIFT score 0.38 0.2 0.42
FatHmm neutral deleterious neutral
FatHmm score -2.46 -3.99 -1.29
FatHmmW neutral neutral neutral
FatHmmW score 2.45 2.39 2.56
PROVEAN deleterious deleterious deleterious
PROVEAN score -3.51 -4.45 -2.56
MutationAssessor high impact high impact low impact
MutationAssessor score 3.77 4.47 1.14
EFIN SP neutral neutral neutral
EFIN SP score 0.62 0.71 0.79
EFIN HD neutral neutral neutral
EFIN HD score 0.49 0.57 0.6
CADD deleterious deleterious deleterious
CADD score 2.27 3.59 1.9
CADD phred 17.98 23.2 15.59
VEST pvalue 0.04 0.02 0.12
VEST FDR 0.35 0.35 0.4
PANTHER neutral disease neutral
PANTHER score 0.47 0.7 0.24
PhD-SNP disease disease disease
PhD-SNP score 0.86 0.93 0.77
SNAP neutral disease neutral
SNAP score 0.42 0.66 0.22
Meta-SNP disease disease neutral
Meta-SNP score 0.69 0.75 0.4
Meta-SNP RI 4 5 2
CAROL neutral deleterious neutral
CAROL score 0.55 0.98 0.78
Condel deleterious neutral neutral
Condel score 0.62 0.12 0.32
COVEC WMV neutral deleterious neutral
COVEC WMV score -2 2 -3
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.35 0.89 0.68
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score -0.04 -2.17 -1.27
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.16 -0.06 0.2
MutationAssessor transf high impact high impact medium impact
MutationAssessor transf score 2.1 2.72 -0.19
CHASM pvalue 0.56 0.54 0.53
CHASM FDR 0.8 0.8 0.8
APOGEE Pathogenic Pathogenic Neutral
APOGEE score 0.53 0.52 0.32
SNPDryad score 0.7 0.96 0.93
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.18 0.36 0.11
Mitoclass.1 damaging damaging neutral
dbSNP 153 id rs397515508 . .
ClinVar March2020 ClinSig Pathogenic . .
ClinVar March2020 ClnDBN Abnormal_electroretinogram|Visual_loss|Leber's_optic_atrophy|Optic_neuropathy . .
ClinVar March2020 ClnAllele id 76427 . .
ClinVar March2020 ClnDSDB Human_Phenotype_Ontology:HP:0000512,MedGen:C0476397|Human_Phenotype_Ontology:HP:0000572,MedGen:C3665386|Human_Phenotype_Ontology:HP:0001112,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|Human_Phenotype_Ontology:HP:0001138,MedGen:C3887709 . .
COSMIC 90 . . .
CPD Frequency 0.15 . .
MITOMAP Allele G3700A . .
MITOMAP Phenotype LHON . .
MITOMAP Homoplasmy + . .
MITOMAP Heteroplasmy - . .
MITOMAP Status Cfrm . .
MITOMAP NRef 5 . .
EVmutation MT-ND1_132A|136V:0.13006;226A:0.095776;221A:0.086424;133L:0.082988;282Y:0.066969 MT-ND1_132A|136V:0.13006;226A:0.095776;221A:0.086424;133L:0.082988;282Y:0.066969 MT-ND1_132A|136V:0.13006;226A:0.095776;221A:0.086424;133L:0.082988;282Y:0.066969
Site A InterP ND1_132 ND1_132 ND1_132
Site B InterP ND4L_57 ND4L_57 ND4L_57
Covariation Score InterP mfDCA_20.0 mfDCA_20.0 mfDCA_20.0
Site A IntraP . . .
Site B IntraP . . .
Covariation Score IntraP . . .
CPD AA ref A . .
CPD AA alt T . .
CPD Aln pos 133 . .
CPD Species name Pongo pygmaeus . .
CPD RefSeq Protein ID NP_008225 . .
CPD Ncbi Taxon id 9600 . .
DDG intra . . .
DDG intra interface . . .
DDG inter . . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.9
  • Conserved:  score > 0.9 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -15, max 10]
  • Neutral:  score > -3
  • Deleterious:  score <= -3
Score:  
0
  [min -3, max 6]
  • Neutral:  score > -1.5
  • Deleterious:  score <= -1.5
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max 35]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.5
  • Pathogenic:  score > 0.5
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend